isoformToGeneExp {IsoformSwitchAnalyzeR} | R Documentation

## Summarize isoform expression to gene level expression.

### Description

This function extract gene expression from isoform expression by for each condition summing the expression of all isoforms belonging to a specific gene.

### Usage

    isoformToGeneExp(
        isoformRepExpression,
        isoformGeneAnnotation=NULL,
        quiet = FALSE
    )

### Arguments

`isoformRepExpression` | A replicate isoform abundace matrix (not log-transformed). The isoform:gene relationship can be provided by either: Having `isoformRepExpression` contain two additional colmns 'isoform_id' and 'gene_id' indicating which isoforms are a part of which gene Using the isoformGeneAnnotation argument. Importantly `isoformRepExpression` must contain isoform ids either as seperate colum called 'isoform_id' or as row.names. The function will figure it out by itself in what combination the annotation is supplied.
`isoformGeneAnnotation` | A data.frame or GRange with two (meta) collumns: 'isoform_id' and 'gene_id' indicating the relationship between isoforms and parent gene.
`quiet` | A logic indicating whether to avoid printing progress messages. Default is FALSE

### Value

This function returns a data.frame where the first column is the gene id followed by the gene expression in all samples.

### Author(s)

Kristoffer Vitting-Seerup

### References

Vitting-Seerup et al. The Landscape of Isoform Switches in Human Cancers. Mol. Cancer Res. (2017).

### Examples

    ### Please note
    # 1) The way of importing files in the following example with
    #       "system.file('pathToFile', package="IsoformSwitchAnalyzeR") is
    #       specialiced to access the sample data in the IsoformSwitchAnalyzeR package
    #       and not somhting you need to do - just supply the string e.g.
    #       "/myAnnotation/isoformsQuantified.gtf" to the functions
    # 2) importRdata directly supports import of a GTF file - just supply the
    #       path (e.g. "/myAnnotation/isoformsQuantified.gtf") to the isoformExonAnnoation argument

    ### Import quantifications
    salmonQuant <- importIsoformExpression(system.file("extdata/", package="IsoformSwitchAnalyzeR"))

    ### Extract gene info
    localAnnotaion <- rtracklayer::import(system.file("extdata/example.gtf.gz", package="IsoformSwitchAnalyzeR"))[,c('transcript_id','gene_id')]
    colnames(localAnnotaion@elementMetadata)[1] <- 'isoform_id'

    ### Summarize to gene level
    geneRepCount <- isoformToGeneExp(
        isoformRepExpression  = salmonQuant$counts,
        isoformGeneAnnotation = localAnnotaion
    )

[Package IsoformSwitchAnalyzeR version 1.4.0 Index]